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Wolfgang Hess @cyanolab.bsky.social · 12d

Riding a train in China, returning from the ISPP 2025 and the Green Carbon conference.

The train station in Qingdao. A light-flooded palace for high-speed trains.

Inside the high-speed train Qingdao-Beijing in China. Riding at more than 300 km/h.

Wolfgang Hess @cyanolab.bsky.social · 12d

„RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics dataset“ rdcu.be/eImcr : 11 authors from 3 labs. Many thanks to all for making this possible!

RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics datasets

Nature Communications - RNA-binding proteins play key roles in post-transcriptional gene regulation. Here, Hemm et al. developed RAPDOR, a widely applicable tool based on Jensen-Shannon Distance...

rdcu.be

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Wolfgang Hess @cyanolab.bsky.social · 12d

To correctly determine a distance there, we used Jensen Shannon Divergence as a metric, which is a symmetrified version of the well-known Kullback–Leibler divergence for comparing distributions.
The GradR data can be searched online at synecho-rapdor.biologie.uni-freiburg.de
@meinbio.bsky.social

Welcome

synecho-rapdor.biologie.uni-freiburg.de

Wolfgang Hess @cyanolab.bsky.social · 12d

For the intuitive analysis + visualization of such datasets we introduce RAPDOR. In contrast to expression profiles, which are compared e.g. by correlation, the results of GradR and similar approaches are naturally displayed as distributions, as the protein fraction in each compartment is measured.

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Wolfgang Hess @cyanolab.bsky.social · 12d

We have been searching for novel RNA-binding proteins and validated, among many candidates, Sll1967 (a possible RlmD homolog), Sll0726 (phosphoglucomutase), Ssl2245 (a putative antitoxin), Slr0711 (possible QueF homolog), and Sll0947 (ribosome-associated inhibitor RaiA/LrtA homolog) as binding RNA.

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Wolfgang Hess @cyanolab.bsky.social · 12d

How to search for unknown RNA-binding proteins? We did GradR in the cyanobacterium Synechocystis 6803. And now our paper „RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics dataset“ is finally out in Nature Communications, here: rdcu.be/eImcr .

RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics datasets

Nature Communications - RNA-binding proteins play key roles in post-transcriptional gene regulation. Here, Hemm et al. developed RAPDOR, a widely applicable tool based on Jensen-Shannon Distance...

rdcu.be

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Wolfgang Hess @cyanolab.bsky.social · Aug 14

Riding a train in Lithuania.

The train is made to look nice. Forest items everywhere

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Wolfgang Hess @cyanolab.bsky.social · Jun 26

¡Muchas gracias, José!

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Wolfgang Hess @cyanolab.bsky.social · Jun 26

Many thanks, Jörg! And it has been a pleasure to visit Göttingen recently!

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Wolfgang Hess @cyanolab.bsky.social · Jun 26

RNA-binding proteins and photosynthesis: The RRM domain–containing protein Rbp3 interacts with ribosomes and the 3’ ends of mRNAs encoding photosynthesis proteins | PNAS www.pnas.org/doi/10.1073/...

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Wolfgang Hess @cyanolab.bsky.social · Jun 26

Inorganic carbon levels regulate growth via SigC signaling cascade in cyanobacteria - Kurkela - New Phytologist - Wiley Online Library nph.onlinelibrary.wiley.com/doi/10.1111/...

Inorganic carbon levels regulate growth via SigC signaling cascade in cyanobacteria

Cyanobacterial growth depends on inorganic carbon (Ci; CO2 and bicarbonate) concentration, but mechanism(s) adjusting photosynthesis and growth according to Ci remain unclear. ΔrpoZ cells lacking th...

nph.onlinelibrary.wiley.com

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Wolfgang Hess @cyanolab.bsky.social · Jun 23

Measuring carbon isotope discrimination and crucial gene expression changes indicated that C. braunii expresses a CO2-concentrating mechanism to cope with these challenges. Supported by @watertoland.bsky.social Details here: nph.onlinelibrary.wiley.com/doi/10.1111/...

Evidence for a CO2‐concentrating mechanism in the model streptophyte green alga Chara braunii

Oxygenic photosynthesis in streptophytic algae, such as Charophyceae, is often impeded by low CO2 levels in aquatic habitats. Consequently, many algal groups evolved a CO2-concentrating mechanism (C...

nph.onlinelibrary.wiley.com

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Wolfgang Hess @cyanolab.bsky.social · Jun 23

They must cope with low CO2 solubility in water, which can limit the CO2 fixation by RubisCO. Moreover, the total pool of inorganic carbon is highly variable in this environment, depending on pH, temperature, and salinity.

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Wolfgang Hess @cyanolab.bsky.social · Jun 23

How are fully submerged algae efficiently fixing carbon?
All organisms performing oxygenic photosynthesis fix CO2 in
the Calvin–Benson–Bassham cycle using RubisCO. But aquatic organisms have a challenge.

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Reposted by Wolfgang Hess

Daan C. Swarts @dcswarts.bsky.social · May 13

Out now: Cyanobacterial Argonautes and Cas4 family nucleases cooperate to interfere with invading DNA
cell.com/molecular-ce...

Most long-A pAgos interfere with invading DNA solo. Why then are cyanobacterial pAgos co-encoded with a Cas4-like protein?

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Reposted by Wolfgang Hess

Chitrang Dani @danichitrang.bsky.social · Mar 18

Just three days left for the deadline for oral abstract submissions for the 15th Workshop on Cyanobacteria at Vanderbilt University (Nashville, TN, USA) - don't miss out!
Workshop dates: 4-7th June 2025. More information: web.cvent.com/event/3d0bd3.... Please share widely!

15th Workshop on Cyanobacteria. Online registration by Cvent

web.cvent.com

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Wolfgang Hess @cyanolab.bsky.social · Mar 3

TIGR-Tas: A new family of modular RNA-guided DNA-targeting systems in prokaryotes and their viruses: www.science.org/doi/10.1126/...

TIGR-Tas: A family of modular RNA-guided DNA-targeting systems in prokaryotes and their viruses

RNA-guided systems provide remarkable versatility, enabling diverse biological functions. Through iterative structural and sequence homology-based mining starting with a guide RNA-interaction domain o...

www.science.org

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Reposted by Wolfgang Hess

Nucleic Acids Research @narjournal.bsky.social · Feb 27

🚨 New #Breakthrough article from @holmqvist-lab.bsky.social: "ProQ prevents mRNA degradation through inhibition of poly(A) polymerase" #RNA #Stability #Degredation #mRNA 📖 Read the full article here: https://doi.org/10.1093/nar/gkaf103

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Wolfgang Hess @cyanolab.bsky.social · Feb 6

Our new Opinion article, now out in Trends in Plant Science is the result of a great collaboration with Conrad Mullineaux and Annegret Wilde freecyano.bsky.social @cyanolab.bsky.social

Annegret Wilde (@freecyano.bsky.social)

cyanobacteriologist from University Freiburg

freecyano.bsky.social

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Wolfgang Hess @cyanolab.bsky.social · Feb 6

Why did chloroplasts retain some genes from their free-living ancestors rather than transferring all of them to the nucleus following endosymbiosis? We suggest that mRNA targeting might play a role.
www.sciencedirect.com/science/arti...

Does mRNA targeting explain gene retention in chloroplasts?

During their evolution from cyanobacteria, plastids have relinquished most of their genes to the host cell nucleus, but have retained a core set of ge…

www.sciencedirect.com

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Reposted by Wolfgang Hess

Sonja-Verena Albers @archaellum.bsky.social · Feb 3

Would you expect that Bacteria use an archaellum for swimming? We didn't, but we found that some Chloroflexota do! Find the story here: www.biorxiv.org/content/10.1...

A little thread below 1/n

Horizontal gene transfer of the functional archaellum machinery to Bacteria

Motility in Archaea is driven by a nanomachinery called the archaellum. So far, archaella have been exclusively described for the archaeal domain; however, a recent study reported the presence of arch...

www.biorxiv.org

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Reposted by Wolfgang Hess

ᐯIᑕTOᖇ ᑎIᘔET, ᗰᗪ @nizet.bsky.social · Jan 25

🅲🅾🅾🅻 🆃🅴🅲🅷🅽🅾🅻🅾🅶🆈

“Bacterial-MERFISH” provides ~1000-fold volumetric expansion of individual cells, charts gene expression in hundreds of thousands of cells, deciphering bacterial single-cell heterogeneity, intracellular transcriptome organization, and bacterial adaptation to µm-scale niches in vivo

Highly multiplexed spatial transcriptomics in bacteria

Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hin...

www.science.org

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Wolfgang Hess @cyanolab.bsky.social · Jan 26

This review has been put together by 12 authors working on multicellularity in bacteria. Many thanks to the DFG by supporting this research through the SPP priority program 2389 “Emergent Functions of Bacterial Multicellularity”.

Wolfgang Hess @cyanolab.bsky.social · Jan 26

Multicellularity is a key feature of complex life, but how to study multicellularity in bacteria and at the single cell level? Use advanced microscopy, MS imaging, flow cytometry, spatial and single-cell transcriptomics, advanced microfluidics and more. See here: journals.asm.org/doi/10.1128/...

Resolving spatiotemporal dynamics in bacterial multicellular populations: approaches and challenges | Microbiology and Molecular Biology Reviews

SUMMARYThe development of multicellularity represents a key evolutionary transition that is crucial for the emergence of complex life forms. Although multicellularity has traditionally been studied in...

journals.asm.org

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Reposted by Wolfgang Hess

CIBSS – Centre for Integrative Biological Signalling Studies @cibss.bsky.social · Jan 10

Mark your calendars for next Tuesday: Tel Aviv University's Prof. Eilon Shani will present a #CRISPR -based toolkit that targets multiple genes at a genome-wide scale, addressing functional overlap in genetic systems and to uncover hidden mechanisms behind hormone transport.
kurzlinks.de/fprn

Sharepic showing Date, Time and Place of Prof. Eilon Shani's CIBSS Seminar talk on "A Multi-targeted genome-scale CRISPR Toolbox to Overcome Functional Redundancy and Reveal Hidden Hormone Transport Mechanisms", Tuesday, January 14th 2025, Lecture Hall, Institute of Biology I, Hauptstr. 1, and online per Zoom.

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